The additional input here is in a topic that is nearly 2 years dead. However, nothing about this part of the tax or employment provisions is changed.

If someone "ran payroll" or had it done for them, and treated the Sole Proprietor as if they are on payroll as an employee, then it all needs to be rolled back. There is no Payroll payment for that Sole Proprietor.

You can have a payment firm make payments to you. You can have them send in money on your behalf. What matters here is what it was called, how it was reported, where it was sent, what is was supposed to be covering.

A Sole Proprietor is not their own employee. There is no FIT, no withholding, Social Security, Medicare, or Unemployment that reported on W2, 941/944 or 940.

A Sole Proprietor, depending on their complete financial picture, might need to send in 1040-Est, or "quarterly estimates" as it is referred to. That is against their 1040, and their Sched C contributes to that picture. Or, they might have a working spouse with a high enough FIT withheld that the Sched C estimates are already in the computation for estimates paid in.

The amount(s) they take from their firm are not Payroll and are not even a taxable event. They draw from the firms funds, because they are the Owner and these are their funds.

Someone being paid through payroll as payroll with all payroll reporting and filings, needs to stop it. It all needs to be reversed, file amended forms, request refunds, etc. Each case needs to be examined for what it is, how long it happened, when it happened, etc.

No, you cannot try to recharacterize payroll payments as personal estimates. What I've successfully done is pointed out when payroll payments got applied to the wrong period (month or quarter or year) and when 940/941 got mixed up, all for the same entity EIN. The IRS was helpful in straightening out that sort of mess. But trying to allocate entity payments under an EIN to personal payments under a SSN is a bit risky for the IRS to accept by phone. If you can get the IRS to do so, you still need to amend payroll reports, issue a W-2c, etc.

Having an EIN is not the problem.